| EGAD00001000220 |
Deep sequencing of CTCs |
454 GS FLX Titanium,Illumina MiSeq |
3 |
| EGAD00001000224 |
Enrichment of CRC |
454 GS FLX Titanium |
2 |
| EGAD00001000225 |
Deep sequencing of KRAS |
454 GS FLX Titanium |
8 |
| EGAD00001000364 |
We performed low coverage whole genome sequencing of plasma DNA from prostate cancer patients to establish copy number profiles on both a genome-wide and a gene-specific level. The data include plasma samples from prostate cacner patients (n=13), non-malignant controls (males, n=10 and females, n=9), plasma samples from pregnancies with aneuploid and euploid fetuses (n=4). Furthermore, we sequenced different tumor samples (n=6) of one patients and a serial dilution of HT29 in a background of normal DNA (n=9). |
Illumina MiSeq |
50 |
| EGAD00001000365 |
In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit. |
Illumina MiSeq |
7 |
| EGAD00001000396 |
We performed serial plasma-Seq analyses on a male who progressed from castration-sensitive to castration-resistant prostate cancer within 10 months following treatment with androgen-deprivation therapy. |
Illumina MiSeq |
2 |
| EGAD00001000688 |
In this study we performed ultra deep sequencing of genes associated with anti-EGFR resistance, such as KRAS, BRAF, PIK3CA, and EGFR in 17 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. |
Illumina MiSeq |
25 |
| EGAD00001000748 |
In this study we performed whole genome sequencing of plasma DNA (plasma-Seq) of 19 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. We demonstrated that development of resistance to anti-EGFR therapies is frequently associated with focal amplifications of KRAS, MET, and ERBB2. We also showed that focal KRAS amplifications can be acquired in tumor genomes of patients under cytotoxic chemotherapy. Furthermore, we provide evidence that specific chromosomal polysomies, such as overrepresentations of 12p and 7p, harboring KRAS and EGFR, respectively, determine responsiveness to anti-EGFR therapy. |
Illumina MiSeq |
19 |
| EGAD00001000761 |
In order to establish copy number profiles from the various samples we prepared libraries and subjected them to whole-genome sequencing at a shallow sequencing depth (0.1x) |
Illumina MiSeq |
14 |
| EGAD00001000762 |
We utilized exome sequencing for DNA obtained from saliva (germline DNA) and the four spatially separated tumor foci and 3 corresponding lymph node metastases |
Illumina HiSeq 2000 |
8 |
| EGAD00001000763 |
We used targeted deep sequencing to accurately establish the allele frequencies of the mutations identified by exome sequencing |
Illumina MiSeq |
23 |
| EGAD00001001009 |
Exome sequencing of peripheral blood from 4 individuals of a family with familial colorectal cancer type X |
Illumina HiSeq 2000 |
4 |
| EGAD00001001010 |
Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2 |
Ion Torrent Proton |
8 |
| EGAD00001001313 |
We enriched a panel of cancer associated genes using the Custom Sure Select Target Enrichment Kit. Identified mutations were validated with deep sequencing in order to assess mutated allele frequencies more accurately. |
Illumina MiSeq |
10 |
| EGAD00001001314 |
Sequence data from L1-amplicon libraries prepared from plasma-DNA from a set of 24 female controls and 18 male controls without malignant disease and samples from patients breast (n= 28) and prostate cancer patients (n=61). |
Illumina MiSeq |
125 |
| EGAD00001002149 |
Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping in plasma DNA of prostate cancer patients |
Illumina MiSeq |
95 |
| EGAD00001002150 |
Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping of corresponding tumor material |
Illumina MiSeq |
8 |
| EGAD00001002215 |
Low coverage whole genome sequencing plasma DNA from 50 male, 54 female non-cancer donors. For the analysis of nucleosomal positioning all data from the non-cancer controls were merged. Furthermore, two patients with metastasized breast cancer were sequenced on a NextSeq with higher depth. |
Illumina MiSeq,NextSeq 550 |
108 |
| EGAD00001002216 |
RNA-Seq on an Ion Torrent Proton of corresponding tumor material of two metastasized breast cancer patients (Breast7, Breast13). |
Ion Torrent Proton |
2 |
| EGAD00001002217 |
Merged file of low-coverage WGS from 179 plasma DNA samples from non-cancer controls and cancer patients for assessment of size distribution of plasma nuclear DNA fragments. |
Illumina MiSeq |
1 |
| EGAD00001002254 |
Single-end sequencing data (trimmed to 60bp) of 104 plasma samples from donors without tumors (male=50; female=54) were merged and used to establish coverage profiles around the TSS and to establish a gene expression prediction algorithm. Dataset includes merged alignements of low coverage whole genome sequencing from plasma DNA from 50 male, 54 female non-cancer donors. Furthermore, 2 patients with metastasized breast cancer were sequenced on a NextSeq with higher depth. |
Illumina MiSeq |
3 |
| EGAD00001003273 |
Low-coverage whole genome sequencing for the establishment of genomewide copy number alterations in pleura effusions and respective primary tumors |
Illumina MiSeq |
20 |
| EGAD00001005343 |
random whole-genome shotgun sequencing of cfDNA in control samples (NPH*) and late-stage cancer samples. First letter denotes primary cancer tissue (C: Colon, B: Breast, P: Prostate) |
Illumina NovaSeq 6000,NextSeq 550 |
41 |
| EGAD00001005761 |
Bevacizumab is an approved anti-angiogenic drug for patients with metastasized colorectal cancer (mCRC) targeting VEGF. The survival benefit of anti-VEGF therapy in mCRC patients is limited to a few months and acquired resistance mechanisms are greatly unknown. Using plasma DNA, we studied the evolution of tumor genomes in a cohort of patients with mCRC (n=150) and observed a recurrent focal amplification (8.7% of cases) on chromosome 13q12.2. Analysis of TCGA data (n=619) suggested an association with later stages, which we confirmed by longitudinal plasma analyses. We defined the minimally amplified region and studied the mechanistic consequences of copy number gain of the involved genes. The amplification of one gene, POLR1D, impacted cell proliferation, resulting in upregulation of VEGFA, an important regulator of angiogenesis which has been implicated in the resistance to bevacizumab. In several patients, we observed the emergence of this 13q12.2 amplicon under bevacizumab treatment, which was invariably associated with evolution of therapy resistance. Hence, we describe a novel resistance mechanism against a widely applied treatment in mCRC patients which will impact clinical management . |
Illumina MiSeq,NextSeq 550 |
38 |
| EGAD00001005804 |
Paired end shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of renal cell carcinoma (RCC) patients (MonRec Cohort) |
Illumina MiSeq,NextSeq 550 |
117 |
| EGAD00001005805 |
Paired end shallow whole genome sequencing (sWGS) data of cell-free DNA from plasma from self-reporting healthy individuals (MonRec Cohort) |
NextSeq 550 |
22 |
| EGAD00001005806 |
Mutation analysis of 10 frequently mutated genes in renal cell carcinoma (BAP1, KDM5C, MET, MTOR, PBRM1, PIK3CA, PTEN, SETD2, TP53, VHL) in plasma DNA of RCC patients using a custom QIASeq panel (MonRec Cohort) |
Illumina MiSeq,NextSeq 550 |
276 |
| EGAD00001005812 |
Whole exome sequencing (WES) of tumor tissues from RCC patients (DIAMOND cohort) |
Illumina HiSeq 4000 |
74 |
| EGAD00001005813 |
A 2.077Mb (57306 probes) personalised capture panel [Tailored Panel Sequencing (TAPAS)] was designed based upon the somatic SNVs identified by WES of RCC patient FF and FFPE tissue samples and applied to cfDNA in plasma and urine. |
Illumina HiSeq 4000 |
62 |
| EGAD00001005814 |
Paired end shallow whole genome sequencing (sWGS) data of cell-free DNA from plasma and urine from RCC patients (DAIMOND cohort) |
Illumina HiSeq 4000 |
106 |
| EGAD00001005815 |
Paired end shallow whole genome sequencing (sWGS) data of tumor tissue from RCC patients (DAIMOND cohort) |
Illumina HiSeq 4000 |
45 |
| EGAD00001006101 |
Paired end (47/98) and single end (51/98) shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of colorectal cancer (CRC) patients. |
Illumina MiSeq,NextSeq 550 |
52 |
| EGAD00001006103 |
Mutation analysis of 17 genes (ALK, APC, BRAF, BRCA1, BRCA2, DPYD, EGFR, ERBB2, KIT, KRAS, MET, NRAS, PDGFRA, RET, ROS1, TP53, UGT1A1) in plasma DNA of CRC patients using the AVENIO ctDNA Targeted Kit. |
NextSeq 550 |
26 |
| EGAD00001006104 |
Mutation analysis in plasma samples with low ctDNA levels using a molecular barcoding technology, i.e. the single target approach SiMSen-seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing). |
Illumina MiSeq,NextSeq 550 |
53 |
| EGAD00001006105 |
Targeted deep sequencing for the KRAS p.Gly12Asp, p.Gly12Val and p.Ala146Thr mutations in plasma samples of CRC patients. |
Illumina MiSeq |
27 |
| EGAD00001006288 |
This is the raw data obtained from shallow whole-genome sequencing of plasma DNA (plasma-Seq) for calling of somatic copy number alterations as well as focal amplifications and deletions from patients with breast, colorectal and non-small cell lung cancer. |
Illumina MiSeq,NextSeq 550 |
48 |
| EGAD00001006301 |
The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 48 plasma samples from patients with breast, colorectal and non-small cell lung cancer. After sequencing 150bp paired-end, reads were aligned to the hg38 genome with the AVENIO Oncology Analysis Software (version 2.0). These files are the deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling. |
NextSeq 550 |
48 |
| EGAD00001006384 |
Shallow whole-genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of metastatic colorectal cancer patients (mCRC). |
Illumina MiSeq,NextSeq 550 |
45 |
| EGAD00001006385 |
Modified Fast Aneuploidy Screening Test-Sequencing System (mFAST-SeqS) was applied to stratify samples based on their overall tumor fraction in cfDNA. |
Illumina MiSeq |
59 |
| EGAD00001006386 |
All baseline samples and when available EOT were processed for high-resolution mutation analysis. We designed a SureSelectXT-HS custom panel (Agilent) covering 68 genes with a total size of 260kb using the Agilent SureDesign platform. |
NextSeq 550 |
44 |
